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A cutscene opens the stage, zooming in from afar to Midair Stadium, which floats above the ground. A blue arena can be seen inside. The camera moves to show special guest spectators Zelda and Peach looking on from the crowd. Mario, in trophy form, is tossed into the arena as the crowd roars, and is transformed into its fighter form. The same happens with Kirby. A versus screen appears with both Kirby and Mario's faces, and the player is allowed to select whom they shall fight as. In Co-op, Player 2 is a color change of whichever character Player 1 picks.

The ending of the first cutscene, where the player selects their character.

The Midair Stadium stage during battle.

The player is then dropped onto a standard arena in a 1-stock match against the other fighter. After the opposing fighter is KO'd, the battle ends.

In the following cutscene, Pit is shown viewing the battle from Skyworld. After this, Mario/Kirby wins the match and revives Kirby/Mario who was turned into a trophy.[1] After the revival, a shadow covers Midair Stadium. The Battleship Halberd descends through dark red clouds, dropping Shadow Bugs into the Stadium, which form Primids. Zelda uses Farore's Wind to warp to Kirby and Mario, and Peach drops down using a parasol. The player is now allowed to select a character for the next segment between Mario, Kirby, Peach and Zelda.

Combat resumes on the same arena as before. The player must face a number of lesser Subspace foes, including Primids, Boom Primids, Sword Primids, and Spaaks.

After all of the enemies are defeated, a new cutscene begins. In the cutscene, the Ancient Minister is introduced as he descends from the Halberd. He drops a Subspace Bomb onto the stadium, and two R.O.B.s activate the device. Mario dashes towards the device in an attempt to deactivate it, but is blown out of Midair Stadium by a cannonball. Kirby turns to watch, hears screaming, and turns back to see Peach and Zelda in cages held by Petey Piranha. Kirby approaches Petey as he roars.

The player must now defeat Petey, the game's first boss. Petey has three attacks. He will either swing Zelda's cage, swing Peach's cage, or leap. All three attacks can be dodged by well-timed jumps. After Petey loses about 2/3 of his health, he will glow red and roar. This indicates a slight increase in the speed of Petey's attacks. To defeat Petey, the player must destroy either Peach's cage or Zelda's cage. Each cage has a separate health bar: attacks to a specific cage decrease its health only. Attacks to Petey himself will damage both cages. Petey dies when the player depletes one of the cage's health bars to zero.

After Petey is defeated, he gets set on fire, and the cages holding the princesses break. Kirby and Zelda/Peach land safely only to watch Wario appear with a Dark Cannon. Wario turns to see a weakened Peach/Zelda and aims the cannon at her[2]. A black arrow comes out of the cannon and pierces her body, turning her into a trophy.

Kirby and Zelda/Peach will attempt to chase after Wario in a bid to save their friend, but Kirby notices that the bomb is about to explode, and then makes his escape riding a Warp Star from Midair Stadium before it is consumed by Subspace, taking Zelda/Peach with him[3].

Mario's right eye is missing as marked by the red circle of this photo.

If the player defeats Petey Piranha in The Great Maze, and then revisits the Midair Stadium, the player will find two platforms floating above the main stage in a similar nature to Pokémon Stadium and Pokémon Stadium 2. Oddly enough, these are never seen outside of the Great Maze.

If the player chooses to play as Kirby in the Kirby vs. Mario match at the beginning of the Subspace Emissary, once the player defeats him, there will be an error in the cutscene which shows Mario turned into a trophy: While the left eye of Mario's trophy is present, the right eye is missing. In all other cutscenes which show Mario's trophy, though, the right eye is present.

In an early trailer of the game, featuring various gameplay clips from both matches and the Subspace Emissary, Mario is shown fighting Petey Piranha as part of the SSE stage. This trailer is available to watch as a movie in the Data tab under the name Game Intro.

Even in the first playthrough, during the Ambush, the player can choose to play as Sheik via Transform, despite the cutscenes picturing Zelda instead.